SYNOPSIS

snap-aligner ,index <input.fa> <output-dir> /[,<options>/]

DESCRIPTION

Welcome to SNAP version 1.0beta.18.

OPTIONS

-s

Seed size (default: 20)

-h

Hash table slack (default: 0.3)

-hg19

Use pre-computed table bias for hg19, which results in better speed, balance, and a smaller index, but only works for the complete human reference.

-Ofactor

This parameter is deprecated and will be ignored.

-tMaxThreads

Specify the maximum number of threads to use. Default is the number of cores.

-B<chars>

Specify characters to use as chromosome name terminators in the FASTA header line; these characters and anything after are not part of the chromosome name. You must specify all characters on a single -B switch. So, for example, with -B_|, the FASTA header line '>chr1|Chromosome 1' would generate a chromosome named 'chr1'. There's a separate flag for indicating that a space is a terminator.

-bSpace

Indicates that the space character is a terminator for chromosome names (see -B above). This may be used in addition to other terminators specified by -B. -B and -bSpace are case sensitive.

-pPadding

Specify the number of Ns to put as padding between chromosomes. This must be as large as the largest edit distance you'll ever use, and there's a performance advantage to have it be bigger than any read you'll process. Default is 500

-HHistogramFile

Build a histogram of seed popularity. This is just for information, it's not used by SNAP.

-exact

Compute hash table sizes exactly. This will slow down index build, but usually will result in smaller indices.

-keysize

The number of bytes to use for the hash table key. Larger values increase SNAP's memory footprint, but allow larger seeds. Default: 4

-large

Build a larger index that's a little faster, particualrly for runs with quick/inaccurate parameters. Increases index size by about 30%, depending on the other index parameters and the contents of the reference genome

-locationSize

The size of the genome locations stored in the index. This can be from 4 to 8 bytes. The locations need to be big enough not only to index the genome, but also to allow some space for representing seeds that occur multiple times. For the human genome, it will fit with four byte locations if the seed size is 19 or larger, but needs 5 (or more) for smaller seeds. Making the location size bigger than necessary will just waste (lots of) space, so unless you're doing something quite unusual, the right answer is 4 or 5. Default is 4

-sm

Use a temp file to work better in smaller memory. This only helps a little, but can be the difference if you're close. In particular, this will generally use less memory than the index will use once it's built, so if this doesn't work you won't be able to use the index anyway. However, if you've got sufficient memory to begin with, this option will just slow down the index build by doing extra, useless IO.